RetrogeneDB ID: retro_sscr_1001

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:78390111..78390495(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RPL32
• Ensembl ID: ENSSSCG00000027637
• Aliases: None
• Description: 60S ribosomal protein L32 [Source:UniProtKB/Swiss-Prot;Acc:Q6QAT0]

Sequence

>retro_sscr_1001
ATGGCCTCTTTCAGACCCCTCATGAAGCCCCAGATCATCAAAAAGAGGACCAAGAAGCTCATCCGGCACCAGTCAGACTA
ACATATCAAAATTAAGTGGAACTGGCAGAAACCCAGAGGCATTGACCACAGGGTGAGTAGCAGGTGCAAGGGCCAGCTCT
TAATGCCCAACACTGGTTATGGGAGCAACCAGAAAATAAAGCCAGTGCTGCCCAGTGGCTTCCGGAAGTTTCTGGTACAC
AGTGTAAAGGAGCTTGAAGTGCTGCTGATGTGCAACAAATCGTACTGTGCTGCGATTGCTCACAATGTCTCTTTCAAGAA
TCGCAAAGCTGTTGTGAAGAGAGTGGCCCAGCTGGCCATCAGGGTCACCAATCCCAACACAAAG

Alignment

ORF - retro_sscr_1001 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.34 %
• Parental protein coverage: 94.81 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGYGSNKKTKHML
          MA..RPL.KP.I.KKRTKK.IRHQSD...KIK.NW.KPRGID.RV..R.KGQ.LMPN.GYGSN.K.K..L
Retrocopy MASFRPLMKPQIIKKRTKKLIRHQSD*HIKIKWNWQKPRGIDHRVSSRCKGQLLMPNTGYGSNQKIKPVL

Parental  PSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAIRVTNPNAR
          PSGFRKFLVH.VKELEVLLMCNKSYCA.IAHNVS.KNRKA.V.R.AQLAIRVTNPN..
Retrocopy PSGFRKFLVHSVKELEVLLMCNKSYCAAIAHNVSFKNRKAVVKRVAQLAIRVTNPNTK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP014902_placenta	0.00 RPM	136.31 RPM
SRP014902_testis	0.14 RPM	449.66 RPM
SRP018288_heart	0.00 RPM	214.97 RPM
SRP018288_kidney	0.00 RPM	188.64 RPM
SRP018288_liver	0.00 RPM	162.15 RPM
SRP018288_lung	0.00 RPM	149.99 RPM
SRP018856_adipose	0.00 RPM	864.32 RPM
SRP035408_brain	0.00 RPM	127.77 RPM
SRP035408_liver	0.00 RPM	100.81 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_1001 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_1001 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_1001 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 133 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014763	3 retrocopies	retro_acar_104, retro_acar_125, retro_acar_67,
Ailuropoda melanoleuca	ENSAMEG00000004583	26 retrocopies	retro_amel_1004, retro_amel_1041, retro_amel_1059, retro_amel_112, retro_amel_1274, retro_amel_1284, retro_amel_13, retro_amel_1394, retro_amel_1450, retro_amel_150, retro_amel_1651, retro_amel_168, retro_amel_1766, retro_amel_1827, retro_amel_1897, retro_amel_274, retro_amel_275, retro_amel_44, retro_amel_573, retro_amel_658, retro_amel_71, retro_amel_776, retro_amel_781, retro_amel_871, retro_amel_892, retro_amel_923,
Bos taurus	ENSBTAG00000015283	10 retrocopies	retro_btau_1102, retro_btau_1391, retro_btau_1568, retro_btau_1645, retro_btau_1728, retro_btau_1764, retro_btau_377, retro_btau_623, retro_btau_631, retro_btau_654,
Choloepus hoffmanni	ENSCHOG00000013534	27 retrocopies	retro_chof_1131, retro_chof_1164, retro_chof_1181, retro_chof_1234, retro_chof_1461, retro_chof_152, retro_chof_1821, retro_chof_1957, retro_chof_2022, retro_chof_205, retro_chof_2090, retro_chof_2146, retro_chof_2242, retro_chof_2265, retro_chof_2301, retro_chof_2410, retro_chof_2509, retro_chof_2527, retro_chof_2606, retro_chof_276, retro_chof_286, retro_chof_313, retro_chof_554, retro_chof_585, retro_chof_607, retro_chof_758, retro_chof_913,
Equus caballus	ENSECAG00000007201	4 retrocopies	retro_ecab_1115, retro_ecab_26, retro_ecab_369, retro_ecab_698,
Loxodonta africana	ENSLAFG00000032737	1 retrocopy	retro_lafr_14,
Macaca mulatta	ENSMMUG00000001340	6 retrocopies	retro_mmul_106, retro_mmul_117, retro_mmul_126, retro_mmul_79, retro_mmul_93, retro_mmul_95,
Mustela putorius furo	ENSMPUG00000017189	4 retrocopies	retro_mputfur_121, retro_mputfur_76, retro_mputfur_8, retro_mputfur_85,
Nomascus leucogenys	ENSNLEG00000004789	12 retrocopies	retro_nleu_1109, retro_nleu_125, retro_nleu_1452, retro_nleu_1642, retro_nleu_193, retro_nleu_224, retro_nleu_2808, retro_nleu_2809, retro_nleu_442, retro_nleu_497, retro_nleu_56, retro_nleu_603,
Otolemur garnettii	ENSOGAG00000028498	24 retrocopies	retro_ogar_129, retro_ogar_1321, retro_ogar_1340, retro_ogar_1360, retro_ogar_1425, retro_ogar_1524, retro_ogar_160, retro_ogar_1683, retro_ogar_1766, retro_ogar_1833, retro_ogar_2032, retro_ogar_2412, retro_ogar_2416, retro_ogar_2515, retro_ogar_3247, retro_ogar_3384, retro_ogar_545, retro_ogar_56, retro_ogar_571, retro_ogar_776, retro_ogar_870, retro_ogar_891, retro_ogar_924, retro_ogar_973,
Pongo abelii	ENSPPYG00000013391	2 retrocopies	retro_pabe_135, retro_pabe_98,
Rattus norvegicus	ENSRNOG00000010746	4 retrocopies	retro_rnor_179, retro_rnor_27, retro_rnor_278, retro_rnor_327,
Sarcophilus harrisii	ENSSHAG00000012782	1 retrocopy	retro_shar_580,
Sus scrofa	ENSSSCG00000027637	9 retrocopies	retro_sscr_1001 , retro_sscr_1054, retro_sscr_107, retro_sscr_1081, retro_sscr_165, retro_sscr_76, retro_sscr_793, retro_sscr_957, retro_sscr_989,